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      Web‐accessible molecular modeling with Rosetta: The Rosetta Online Server that Includes Everyone (ROSIE)

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          Abstract

          The Rosetta molecular modeling software package provides a large number of experimentally validated tools for modeling and designing proteins, nucleic acids, and other biopolymers, with new protocols being added continually. While freely available to academic users, external usage is limited by the need for expertise in the Unix command line environment. To make Rosetta protocols available to a wider audience, we previously created a web server called Rosetta Online Server that Includes Everyone (ROSIE), which provides a common environment for hosting web‐accessible Rosetta protocols. Here we describe a simplification of the ROSIE protocol specification format, one that permits easier implementation of Rosetta protocols. Whereas the previous format required creating multiple separate files in different locations, the new format allows specification of the protocol in a single file. This new, simplified protocol specification has more than doubled the number of Rosetta protocols available under ROSIE. These new applications include p K a determination, lipid accessibility calculation, ribonucleic acid redesign, protein‐protein docking, protein‐small molecule docking, symmetric docking, antibody docking, cyclic toxin docking, critical binding peptide determination, and mapping small molecule binding sites. ROSIE is freely available to academic users at http://rosie.rosettacommons.org.

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          Author and article information

          Contributors
          jgray@jhu.edu
          Journal
          Protein Sci
          Protein Sci
          10.1002/(ISSN)1469-896X
          PRO
          Protein Science : A Publication of the Protein Society
          John Wiley and Sons Inc. (Hoboken )
          0961-8368
          1469-896X
          27 October 2017
          January 2018
          : 27
          : 1 , Special Issue on Tools for Protein Science ( doiID: 10.1002/pro.v27.1 )
          : 259-268
          Affiliations
          [ 1 ] Department of Chemistry Vanderbilt University Nashville Tennessee
          [ 2 ] Department of Chemical and Biomolecular Engineering The Johns Hopkins University Baltimore Maryland
          [ 3 ] Department of Biochemistry Stanford University Stanford California
          [ 4 ] Department of Physics Stanford University Stanford California
          [ 5 ] Program in Molecular Biophysics, The Johns Hopkins University Baltimore Maryland
          Author notes
          [*] [* ] Correspondence to: Jeffrey J. Gray, Johns Hopkins University, 208 Maryland Hall, Baltimore, MD 21218. E‐mail: jgray@ 123456jhu.edu
          Author information
          http://orcid.org/0000-0001-6380-2324
          Article
          PMC5734271 PMC5734271 5734271 PRO3313
          10.1002/pro.3313
          5734271
          28960691
          c156d390-509b-4a50-a36c-f2a89e5da637
          © 2017 The Protein Society
          History
          : 25 July 2017
          : 21 September 2017
          : 25 September 2017
          Page count
          Figures: 2, Tables: 3, Pages: 10, Words: 6454
          Funding
          Funded by: RosettaCommons and the National Institutes of Health
          Award ID: R01‐GM073151
          Categories
          Tools for Protein Science
          Tools for Protein Science
          Custom metadata
          2.0
          pro3313
          January 2018
          Converter:WILEY_ML3GV2_TO_NLMPMC version:5.2.8 mode:remove_FC converted:18.12.2017

          prediction,design,molecular modeling,web server
          prediction, design, molecular modeling, web server

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